Microevolution of Renibacterium salmoninarum: evidence for intercontinental dissemination associated with fish movements

Authors: BRYNILDSRUD, OLA - Norwegian School Of Veterinary Sciences; FEIL, EDWARD - University Of Bath; BOHLIN, JON - Norwegian School Of Veterinary Sciences; CASTILLO-RAMIREZ, SANTIAGO - University Of Bath; COLQUHOUN, DUNCHAN - Norwegian Veterinary Institute; MCCARTHY, UNA - Marine Scotland; MATEJUSOVA, IVETA - Marine Scotland; RHODES, LINDA - National Oceanic & Atmospheric Administration (NOAA); Wiens, Gregory - Greg; VERNER-JEFFREYS, DAVID - Centre For Environment, Fisheries And Aquaculture Science (CEFAS)

Submitted to: The ISME Journal: Multidisciplinary Journal of Microbial Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/9/2013
Publication Date: 10/31/2013
Publication URL: http://handle.nal.usda.gov/10113/59376
Citation: Brynildsrud, O., Feil, E.J., Bohlin, J., Castillo-Ramirez, S., Colquhoun, D., Mccarthy, U., Matejusova, I.M., Rhodes, L., Wiens, G.D., Verner-Jeffreys, D.W. 2013. Microevolution of Renibacterium salmoninarum: evidence for intercontinental dissemination associated with fish movements. The ISME Journal: Multidisciplinary Journal of Microbial Ecology. 8: 746-756. DOI: 10.1038/ismej.2013.186.

Interpretive Summary: Salmonid bacterial kidney disease is caused by the pathogen Renibacterium salmoninarum. This bacterium infects multiple species of salmon and trout and causes economically significant levels of mortality at aquaculture facilities in both the U.S. and Europe. We have previously determined the complete genome sequence of this bacterium; however, limited information is available regarding the genetic variation between strains and whether outbreaks in different species of fish are caused by the same or different strains. In this manuscript, a total of 68 isolates were sequenced that were obtained from eight host species of salmon and trout obtained from the U.S., Canada, Norway, Scotland, England and Wales . A total of 3844 polymorphisms in the DNA sequence were identified. Based on these sequence differences, a phylogenetic tree was calculated and two broad groups (lineages) of the pathogen were identified. Lineage 1 (90% of the isolates) was obtained from all eight host species, while lineage 2 was only identified from Atlantic salmon and Brown trout. The time that the two lineages became separate was estimated to be approximately 1239 years ago. Lineage 1 isolates are globally distributed while lineage 2 isolates appear to be restricted to the UK and Norway. The global distribution of lineage 1 may be due to transport of fish, gametes or fish feed. The genetic data also indicate that some outbreaks are caused by identical pathogen strains, while other outbreaks may be due to the coexistence of multiple strains. The genetic information reported in this paper will aid future outbreak investigation and improve our understanding of bacterial kidney disease transmission.

Technical Abstract: Renibacterium salmoninarum is the causative agent of bacterial kidney disease, a major pathogen of salmonid fish species worldwide. Very low levels of intra-species genetic diversity have hampered efforts to understand the transmission dynamics and recent evolutionary history of this Gram-positive bacterium. We exploited recent advances in Next Generation Sequencing (NGS) technology to generate genome wide single nucleotide polymorphism (SNP) data from 68 diverse R. salmoninarum isolates representing broad geographical and temporal ranges and different host species. Phylogenetic analysis robustly delineated two lineages (lineage 1 and lineage 2); futhermore, dating analysis estimated that the time to the most recent ancestor of all the isolates is 1239 years ago and, therefore, the two lineages started to diverge allopatrically at some point in time after this date. Our data reveals the intercontinental spread of lineage 1 over the last century, concurrent with anthropogenic movement of live fish, feed and ova for aquaculture purposes and stocking of recreational fisheries, whilst lineage 2 appears to have been endemic in wild Eastern Atlantic salmonid stocks prior to commercial activity. The high resolution of the SNP based analyses allowed us to separate closely related isolates linked to neighbouring fish farms, indicating they formed part of single outbreaks. We were able to demonstrate that the main lineage 1 subgroup of R. salmoninarum isolated from Norway and the UK likely represent an introduction to these areas around 40 years ago. This study demonstrates the promise of this technology for analysis of micro and medium scale evolutionary relationships in veterinary and environmental microorganisms, as well as human pathogens.